biology

Remix of IO-Rodeo's colorimeter, reusing their cuvette holder and led-sensor hardware. This version runs on ESPs, offering basic control through buttons, and advanced control through a web UI, websockets, and serial.

A Flutter app for visualizing 3D molecular structures from CIF files in the PDB database.

SeqExtract searches annotated genomes for keywords and extract corresponding fasta records

AmpCheck investigates primer/probe - template matching and return amplicon related information.

https://dnarna.gitlab.io/ampcheck

RepeatGrower identify repeating k-mers in a genome and grows them until their occurrences decline.

This is the script for the bacterial FHN model that we reported in Startford et al., PNAS (2019). https://doi.org/10.1073/pnas.1901788116

Microscope Image Annotator (MIA) provides command-line driven microscope image annotation, including scales, labels and image post processing.

This script contains a collection of functions designed to put EthoVision tracks into a more usable format for further data analysis. This includes interpolating, smoothing, extracting data and metadata and writing them out as separate csv files.

Bioinformatics - Segmentation of biofilm images using OpenCV library.

A parametric design for a test rig for different combinations of LEE or Rosco gel filters allowing LEDs and photodetectors to be set up with different filter combinations and either a cuvette or capillary containing the sample.

The Noble Ape Simulation was started in 1996. It features a number of autonomous simulation components including: landscape, biological, weather, sentient creature, a simple intelligent-agent scripting language (ApeScript). http://www.nobleape.com/

FFIND is a data-agnostic, scalable web platform with capability to integrate image and non-image data types (transcriptomics, flow cytometry, electrophysiology) into a user interface tailored to project-specific goals.

CommunityYeastract database and web php front-end

Solves genetic problems and simulates population

Larval fish growth model

Haruspex is a Convolutional Neural Network capable of recognizing and predicting secondary structure elements and nucleotides in Cryo-EM reconstruction density.